Get accepted canonical names and taxonomy for a given species name
Source:R/get_gbif_taxonomy.R
get_gbif_taxonomy.RdThe function maps user provided names to accepted species names.
Usage
get_gbif_taxonomy(
x,
subspecies = TRUE,
higherrank = FALSE,
verbose = FALSE,
fuzzy = TRUE,
conf_threshold = 90,
resolve_synonyms = TRUE
)Arguments
- x
a character string or vector of species names.
- subspecies
logical. If TRUE (default), the given name is resolved to subspecies epithet, otherwise it will be mapped to species level.
- higherrank
logical. If FALSE (default), it will not allow remapping of unknown species names to higher taxon ranks (e.g. genus).
- verbose
logical. If FALSE (default), warnings and messages are suppressed.
- fuzzy
logical. Defaults to TRUE to deal with misspelled names. May produce wrong assignments in case of very similar taxon names. If FALSE (default), names are only resolved to exactly matching taxa on GBIF taxonomy service.
- conf_threshold
numerical, ranging from 0 to 100 (default value = 90). Defines the confidence level of the request to be accepted. To cover for misspellings and errors, could go as low as 50.
- resolve_synonyms
logical. If TRUE (default), user provided synonyms are mapped to the accepted names on GBIF taxonomy service.
Value
a data.frame mapping the user supplied names to the accepted taxon names and higher taxonomic information (kingdom, phylum, class, order, family, genus).
Details
The function relies on package 'taxize' by Scott Chamberlain. It
uses the spell-checking and fuzzy matching algorithms provided by Global
Names Resolver (taxize::gnr_resolve()) and forwards synonyms to the
accepted names as provided by GBIF Backbone Taxonomy
(taxize::get_gbif_id_()).
If 'synonym' is returned as TRUE, the user provided name has been identified as a synonym and was mapped to an accepted name.
The field confidence reports the confidence of the matching procedure
performed by the function get_gbifid_() of the package 'taxize'. The
taxonID is a globally valid URI that links to the taxon description of the
GBIF backbone taxonomy.
Examples
get_gbif_taxonomy(c("Chorthippus albomarginatus", "Chorthippus apricarius",
"Chorthippus biguttulus", "Chorthippus dorsatus", "Chorthippus montanus",
"Chorthippus parallelus", "Chrysochraon dispar", "Conocephalus dorsalis",
"Conocephalus fuscus", "Decticus verrucivorus", "Euthystira brachyptera",
"Gomphocerippus rufus", "Gryllus campestris", "Metrioptera roeselii",
"Omocestus viridulus", "Phaneroptera falcata", "Platycleis albopunctata",
"Spec", "Stenobothrus lineatus", "Stenobothrus stigmaticus",
"Stethophyma grossum", "Tetrix kraussi", "Tetrix subulata",
"Tetrix tenuicornis", "Tetrix undulata", "Tettigonia cantans",
"Tettigonia viridissima")
)
#> verbatimScientificName synonym scientificName
#> 1 Chorthippus albomarginatus FALSE Chorthippus albomarginatus
#> 2 Chorthippus apricarius FALSE Chorthippus apricarius
#> 3 Chorthippus biguttulus FALSE Chorthippus biguttulus
#> 4 Chorthippus dorsatus FALSE Chorthippus dorsatus
#> 5 Chorthippus montanus FALSE <NA>
#> 6 Chorthippus parallelus TRUE Pseudochorthippus parallelus
#> 7 Chrysochraon dispar FALSE Chrysochraon dispar
#> 8 Conocephalus dorsalis FALSE Conocephalus dorsalis
#> 9 Conocephalus fuscus FALSE Conocephalus fuscus
#> 10 Decticus verrucivorus FALSE Decticus verrucivorus
#> 11 Euthystira brachyptera FALSE Euthystira brachyptera
#> 12 Gomphocerippus rufus FALSE Gomphocerippus rufus
#> 13 Gryllus campestris FALSE Gryllus campestris
#> 14 Metrioptera roeselii TRUE Roeseliana roeselii
#> 15 Omocestus viridulus FALSE Omocestus viridulus
#> 16 Phaneroptera falcata FALSE Phaneroptera falcata
#> 17 Platycleis albopunctata FALSE Platycleis albopunctata
#> 18 Spec FALSE <NA>
#> 19 Stenobothrus lineatus FALSE Stenobothrus lineatus
#> 20 Stenobothrus stigmaticus FALSE Stenobothrus stigmaticus
#> 21 Stethophyma grossum FALSE Stethophyma grossum
#> 22 Tetrix kraussi FALSE Tetrix kraussi
#> 23 Tetrix subulata FALSE Tetrix subulata
#> 24 Tetrix tenuicornis FALSE Tetrix tenuicornis
#> 25 Tetrix undulata FALSE Tetrix undulata
#> 26 Tettigonia cantans FALSE Tettigonia cantans
#> 27 Tettigonia viridissima FALSE Tettigonia viridissima
#> author taxonRank confidence kingdom phylum class
#> 1 (De Geer, 1773) species 99 Animalia Arthropoda Insecta
#> 2 (Linnaeus, 1758) species 97 Animalia Arthropoda Insecta
#> 3 (Linnaeus, 1758) species 97 Animalia Arthropoda Insecta
#> 4 (Zetterstedt, 1821) species 97 Animalia Arthropoda Insecta
#> 5 <NA> highertaxon NA <NA> <NA> <NA>
#> 6 (Zetterstedt, 1821) species 99 Animalia Arthropoda Insecta
#> 7 (Germar, 1834) species 99 Animalia Arthropoda Insecta
#> 8 (Latreille, 1804) species 97 Animalia Arthropoda Insecta
#> 9 (Fabricius, 1793) species 97 Animalia Arthropoda Insecta
#> 10 (Linnaeus, 1758) species 97 Animalia Arthropoda Insecta
#> 11 (Ocskay, 1826) species 99 Animalia Arthropoda Insecta
#> 12 (Linnaeus, 1758) species 99 Animalia Arthropoda Insecta
#> 13 Linnaeus, 1758 species 97 Animalia Arthropoda Insecta
#> 14 (Hagenbach, 1822) species 99 Animalia Arthropoda Insecta
#> 15 (Linnaeus, 1758) species 97 Animalia Arthropoda Insecta
#> 16 (Poda, 1761) species 97 Animalia Arthropoda Insecta
#> 17 (Goeze, 1778) species 97 Animalia Arthropoda Insecta
#> 18 <NA> species NA <NA> <NA> <NA>
#> 19 (Panzer, 1796) species 97 Animalia Arthropoda Insecta
#> 20 (Rambur, 1838) species 97 Animalia Arthropoda Insecta
#> 21 (Linnaeus, 1758) species 99 Animalia Arthropoda Insecta
#> 22 Saulcy, 1888 species 99 Animalia Arthropoda Insecta
#> 23 (Linnaeus, 1758) species 97 Animalia Arthropoda Insecta
#> 24 (Sahlberg, 1891) species 97 Animalia Arthropoda Insecta
#> 25 (Sowerby, 1806) species 97 Animalia Arthropoda Insecta
#> 26 (Fuessly, 1775) species 97 Animalia Arthropoda Insecta
#> 27 (Linnaeus, 1758) species 99 Animalia Arthropoda Insecta
#> order family genus taxonomy
#> 1 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy
#> 2 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy
#> 3 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy
#> 4 Orthoptera Acrididae Chorthippus GBIF Backbone Taxonomy
#> 5 <NA> <NA> <NA> GBIF Backbone Taxonomy
#> 6 Orthoptera Acrididae Pseudochorthippus GBIF Backbone Taxonomy
#> 7 Orthoptera Acrididae Chrysochraon GBIF Backbone Taxonomy
#> 8 Orthoptera Tettigoniidae Conocephalus GBIF Backbone Taxonomy
#> 9 Orthoptera Tettigoniidae Conocephalus GBIF Backbone Taxonomy
#> 10 Orthoptera Tettigoniidae Decticus GBIF Backbone Taxonomy
#> 11 Orthoptera Acrididae Euthystira GBIF Backbone Taxonomy
#> 12 Orthoptera Acrididae Gomphocerippus GBIF Backbone Taxonomy
#> 13 Orthoptera Gryllidae Gryllus GBIF Backbone Taxonomy
#> 14 Orthoptera Tettigoniidae Roeseliana GBIF Backbone Taxonomy
#> 15 Orthoptera Acrididae Omocestus GBIF Backbone Taxonomy
#> 16 Orthoptera Tettigoniidae Phaneroptera GBIF Backbone Taxonomy
#> 17 Orthoptera Tettigoniidae Platycleis GBIF Backbone Taxonomy
#> 18 <NA> <NA> <NA> GBIF Backbone Taxonomy
#> 19 Orthoptera Acrididae Stenobothrus GBIF Backbone Taxonomy
#> 20 Orthoptera Acrididae Stenobothrus GBIF Backbone Taxonomy
#> 21 Orthoptera Acrididae Stethophyma GBIF Backbone Taxonomy
#> 22 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy
#> 23 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy
#> 24 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy
#> 25 Orthoptera Tetrigidae Tetrix GBIF Backbone Taxonomy
#> 26 Orthoptera Tettigoniidae Tettigonia GBIF Backbone Taxonomy
#> 27 Orthoptera Tettigoniidae Tettigonia GBIF Backbone Taxonomy
#> taxonID
#> 1 http://www.gbif.org/species/1708567
#> 2 http://www.gbif.org/species/1708601
#> 3 http://www.gbif.org/species/1708251
#> 4 http://www.gbif.org/species/1708512
#> 5 <NA>
#> 6 http://www.gbif.org/species/7792296
#> 7 http://www.gbif.org/species/1700841
#> 8 http://www.gbif.org/species/1683331
#> 9 http://www.gbif.org/species/1683067
#> 10 http://www.gbif.org/species/1690685
#> 11 http://www.gbif.org/species/1701343
#> 12 http://www.gbif.org/species/1700023
#> 13 http://www.gbif.org/species/1716462
#> 14 http://www.gbif.org/species/4402879
#> 15 http://www.gbif.org/species/1710755
#> 16 http://www.gbif.org/species/1686243
#> 17 http://www.gbif.org/species/1685298
#> 18 <NA>
#> 19 http://www.gbif.org/species/1710962
#> 20 http://www.gbif.org/species/1710986
#> 21 http://www.gbif.org/species/1711091
#> 22 http://www.gbif.org/species/9055856
#> 23 http://www.gbif.org/species/1681124
#> 24 http://www.gbif.org/species/1681181
#> 25 http://www.gbif.org/species/1681247
#> 26 http://www.gbif.org/species/8347376
#> 27 http://www.gbif.org/species/1692898
#> warnings
#> 1
#> 2
#> 3
#> 4
#> 5 No matching species concept!
#> 6 A synonym was mapped to the accepted species concept!
#> 7
#> 8
#> 9
#> 10
#> 11
#> 12
#> 13
#> 14 A synonym was mapped to the accepted species concept!
#> 15
#> 16
#> 17
#> 18 Check spelling or lower confidence threshold!
#> 19
#> 20
#> 21
#> 22
#> 23
#> 24
#> 25
#> 26
#> 27
get_gbif_taxonomy("Vicia")
#> verbatimScientificName synonym scientificName author taxonRank confidence
#> 1 Vicia FALSE Vicia L. genus 94
#> kingdom phylum class order family genus
#> 1 Plantae Tracheophyta Magnoliopsida Fabales Fabaceae Vicia
#> taxonomy taxonID warnings
#> 1 GBIF Backbone Taxonomy http://www.gbif.org/species/2974751